Abstract Autophagy, a key host defense pathway, has an essential role in both innate and adaptive immunity. However, many microbes have evolved mechanisms to evade, subvert, or exploit autophagy. Bacterial and viral pathogens can block autophagosome fusion with lysosomes to evade degradation, or utilize nutrients in such vesicles. It has been demonstrated that stimulation of autophagic pathways in macrophages causes mycobacterial phagosomes to mature into phagolysosomes, which can then overcome the trafficking block imposed by Mycobacterium tuberculosis. Thus, induction of autophagy can suppress intracellular survival of mycobacteria. We hypothesize that mycobacterial virulence factors mediate autophagy evasion in order to ensure survival within the infected macrophages. The identification and characterization of such virulence factors will allow us to understand the mechanisms by which autophagy affects the outcome of host-microbe interactions and immune responses. Through loss-of-function screening of mycobacteria using transposon mutant screening, we were able to identify thirteen chromosomal regions responsible for manipulating mycobacterial infection-induced autophagy. Remarkably, six of these regions contain genes belonging to the PE/PPE protein family that are especially abundant in pathogenic mycobacteria and have been shown to play diverse roles in mycobacterial pathogenesis and in modulating critical innate immune pathways. However, no PE/PPE proteins are known to be associated with autophagy pathways. Thus, the goals of this project are to investigate the roles and mechanisms of a subset of PE/PPE proteins and to determine the consequences of autophagic degradation of mycobacteria on innate and adaptive immunity. Increased knowledge of M. tuberculosis infection-induced autophagy presents an opportunity to uncover new and promising therapeutics against tuberculosis to prevent mycobacterial infection and survival within the host. Additionally, the pro- autophagic mutants generated in this study may have significant application in the development of effective, safe and persistent TB vaccines.